matsci-parse 0.0.1

package/README.md

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+A library to unify and interconvert between common material science files types.

package/dist/main.js

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+class S {
+  constructor(e, t, o = {}) {
+    this.speciesIndex = e, this.cart = t, this.props = o;
+  }
+  getProp(e) {
+    return this.props[e];
+  }
+  setProp(e, t) {
+    this.props[e] = t;
+  }
+}
+function I(n) {
+  return n.sites.some((e) => Array.isArray(e.props.selectiveDynamics));
+}
+class x {
+  constructor({
+    lattice: e,
+    species: t,
+    sites: o
+  }) {
+    this.lattice = this._validateLattice(e), this.species = this._validateSpecies(t), this.sites = this._validateSites(o);
+  }
+  // ---------- Simple methods ----------
+  get numSites() {
+    return this.sites.length;
+  }
+  site(e) {
+    return this.sites[e];
+  }
+  cartCoords(e) {
+    return this.sites[e].cart;
+  }
+  siteSpecies(e) {
+    return this.species[this.sites[e].speciesIndex];
+  }
+  get elements() {
+    return this.species;
+  }
+  addSite(e, t) {
+    this._validateSpeciesIndex(e), this.sites.push(new S(e, t));
+  }
+  removeSite(e) {
+    this.sites.splice(e, 1);
+  }
+  // ---------- Internal validation ----------
+  _validateLattice(e) {
+    if (!Array.isArray(e) || e.length !== 3)
+      throw new Error("Lattice must be a 3x3 matrix");
+    return e.forEach((t) => {
+      if (!Array.isArray(t) || t.length !== 3)
+        throw new Error("Lattice vectors must be length 3");
+    }), e;
+  }
+  _validateSpecies(e) {
+    if (!Array.isArray(e)) throw new Error("Species must be an array");
+    return e.forEach((t) => {
+      if (typeof t != "string")
+        throw new Error("Species entries must be strings");
+    }), e;
+  }
+  _validateSites(e) {
+    if (!Array.isArray(e)) throw new Error("Sites must be an array");
+    return e.map((t) => {
+      if (t instanceof S) return t;
+      if (typeof t == "object" && typeof t.speciesIndex == "number" && Array.isArray(t.cart) && t.cart.length === 3)
+        return this._validateSpeciesIndex(t.speciesIndex), new S(
+          t.speciesIndex,
+          t.cart,
+          t.props ?? {}
+        );
+      throw new Error(
+        "Each site must be a Site instance or a valid site object"
+      );
+    });
+  }
+  _validateSpeciesIndex(e) {
+    if (e < 0 || e >= this.species.length)
+      throw new Error("speciesIndex out of bounds");
+  }
+}
+function A(n) {
+  const e = [], t = I(n);
+  e.push("Generated by CrystalStructure"), e.push("1.0"), n.lattice.forEach((s) => {
+    e.push(s.map((p) => p.toFixed(10)).join(" "));
+  });
+  const o = Array.from(
+    new Set(n.sites.map((s) => n.species[s.speciesIndex]))
+  ), i = o.map(
+    (s) => n.sites.filter((p) => n.species[p.speciesIndex] === s).length
+  );
+  return e.push(o.join(" ")), e.push(i.join(" ")), t && e.push("Selective dynamics"), e.push("Cartesian"), o.forEach((s) => {
+    n.sites.filter((p) => n.species[p.speciesIndex] === s).forEach((p) => {
+      const a = p.cart.map((h) => h.toFixed(10)).join(" ");
+      if (t) {
+        const d = (Array.isArray(p.props?.selectiveDynamics) ? p.props.selectiveDynamics : [!0, !0, !0]).map((u) => u ? "T" : "F").join(" ");
+        e.push(`${a} ${d}`);
+      } else
+        e.push(a);
+    });
+  }), e.join(`
+`);
+}
+function j(n) {
+  const e = n.trim().split(/\r?\n/).map((l) => l.trim()).filter((l) => l.length > 0);
+  let t = 0;
+  t++;
+  const o = parseFloat(e[t++]), i = [];
+  for (let l = 0; l < 3; l++)
+    i.push(
+      e[t++].split(/\s+/).map((y) => parseFloat(y) * o)
+    );
+  let s = e[t].trim(), p;
+  /^[A-Za-z]/.test(s) && (p = s.split(/\s+/), t++);
+  const a = e[t++].split(/\s+/).map(Number);
+  p || (p = a.map((l, y) => `X${y + 1}`));
+  let h = !1;
+  e[t]?.toLowerCase().startsWith("s") && (h = !0, t++);
+  const u = e[t++].toLowerCase().startsWith("d"), m = [];
+  return p.forEach((l, y) => {
+    for (let r = 0; r < a[y]; r++) {
+      const c = e[t++].split(/\s+/).map(Number);
+      let f;
+      u ? f = [
+        c[0] * i[0][0] + c[1] * i[1][0] + c[2] * i[2][0],
+        c[0] * i[0][1] + c[1] * i[1][1] + c[2] * i[2][1],
+        c[0] * i[0][2] + c[1] * i[1][2] + c[2] * i[2][2]
+      ] : f = c.slice(0, 3);
+      let w = {};
+      if (h) {
+        const g = e[t - 1].split(/\s+/).slice(3, 6).map((v) => v.toUpperCase() === "T");
+        g.length === 3 && (w.selectiveDynamics = g);
+      }
+      m.push(new S(y, f, w));
+    }
+  }), new x({
+    lattice: i,
+    species: p,
+    sites: m
+  });
+}
+function C(n) {
+  const e = [];
+  return e.push("CRYSTAL"), e.push("PRIMVEC"), n.lattice.forEach((t) => {
+    e.push(t.map((o) => o.toFixed(10)).join(" "));
+  }), e.push("PRIMCOORD"), e.push(`${n.numSites} 1`), n.sites.forEach((t) => {
+    const o = n.species[t.speciesIndex];
+    e.push(`${o} ${t.cart.map((i) => i.toFixed(10)).join(" ")}`);
+  }), e.join(`
+`);
+}
+function D(n) {
+  const e = n.trim().split(/\r?\n/).map((a) => a.trim()).filter((a) => a.length > 0), t = [], o = [], i = [];
+  let s = 0;
+  for (; s < e.length && e[s].toUpperCase() !== "PRIMVEC"; ) s++;
+  if (s === e.length) throw new Error("PRIMVEC block not found in XSF");
+  s++;
+  for (let a = 0; a < 3; a++)
+    t.push(e[s++].split(/\s+/).map(Number));
+  for (; s < e.length && e[s].toUpperCase() !== "PRIMCOORD"; ) s++;
+  if (s === e.length) throw new Error("PRIMCOORD block not found in XSF");
+  s++;
+  const [p] = e[s++].split(/\s+/).map(Number);
+  for (let a = 0; a < p; a++) {
+    const h = e[s++].split(/\s+/), d = h[0], u = h.slice(1, 4).map(Number);
+    let m = o.indexOf(d);
+    m === -1 && (o.push(d), m = o.length - 1), i.push(new S(m, u));
+  }
+  return new x({ lattice: t, species: o, sites: i });
+}
+function F(n) {
+  const e = [], t = n.sites.length;
+  e.push(String(t));
+  const o = I(n), i = n.lattice, s = [
+    i[0][0],
+    i[1][0],
+    i[2][0],
+    i[0][1],
+    i[1][1],
+    i[2][1],
+    i[0][2],
+    i[1][2],
+    i[2][2]
+  ].join(" "), p = [
+    "species:S:1",
+    "pos:R:3",
+    o ? "selectiveDynamics:L:3" : null
+  ].filter(Boolean).join(":");
+  e.push(`Lattice="${s}" Properties=${p}`);
+  for (const a of n.sites) {
+    const h = n.species[a.speciesIndex], [d, u, m] = a.cart;
+    let l = `${h} ${d.toFixed(10)} ${u.toFixed(10)} ${m.toFixed(10)}`;
+    if (o) {
+      const y = Array.isArray(a.props?.selectiveDynamics) ? a.props.selectiveDynamics : [!0, !0, !0];
+      l += " " + y.map((r) => r ? "T" : "F").join(" ");
+    }
+    e.push(l);
+  }
+  return e.join(`
+`);
+}
+function L(n) {
+  const e = n.trim().split(/\r?\n/).map((r) => r.trim()).filter((r) => r.length > 0);
+  let t = 0;
+  const o = parseInt(e[t++], 10);
+  if (!Number.isFinite(o))
+    throw new Error("Invalid XYZ: first line must be atom count");
+  const i = e[t++], s = {}, p = /(\w+)=(".*?"|\S+)/g;
+  for (const r of i.matchAll(p)) {
+    let c = r[2];
+    c.startsWith('"') && (c = c.slice(1, -1)), s[r[1]] = c;
+  }
+  let a;
+  if (s.Lattice) {
+    const r = s.Lattice.split(/\s+/).map(Number);
+    if (r.length !== 9) throw new Error("Invalid Lattice in extended XYZ");
+    a = [
+      [r[0], r[3], r[6]],
+      [r[1], r[4], r[7]],
+      [r[2], r[5], r[8]]
+    ];
+  } else
+    throw new Error("Lattice must be present in extended XYZ format");
+  let h = 0, d = 1, u = null;
+  if (s.Properties) {
+    const r = s.Properties.split(":");
+    let c = 0;
+    for (let f = 0; f < r.length; f += 3) {
+      const w = r[f], g = parseInt(r[f + 2], 10);
+      w === "species" && (h = c), w === "pos" && (d = c), w === "selectiveDynamics" && (u = c), c += g;
+    }
+  }
+  const m = [], l = /* @__PURE__ */ new Map(), y = [];
+  for (let r = 0; r < o; r++) {
+    const c = e[t++].split(/\s+/), f = c[h];
+    l.has(f) || (l.set(f, m.length), m.push(f));
+    const w = l.get(f), g = c.slice(d, d + 3).map(Number), v = {};
+    if (u !== null) {
+      const E = c.slice(u, u + 3).map((b) => b.toUpperCase() === "T");
+      E.length === 3 && (v.selectiveDynamics = E);
+    }
+    y.push(new S(w, g, v));
+  }
+  return new x({ lattice: a, species: m, sites: y });
+}
+export {
+  x as CrystalStructure,
+  S as Site,
+  j as poscarToStructure,
+  A as structureToPoscar,
+  C as structureToXsf,
+  F as structureToXyz,
+  D as xsfToStructure,
+  L as xyzToStructure
+};

package/package.json

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+{
+  "name": "matsci-parse",
+  "version": "0.0.1",
+  "type": "module",
+  "main": "dist/main.js",
+  "module": "dist/main.js",
+  "files": [
+    "dist"
+  ],
+  "scripts": {
+    "dev": "vite",
+    "build": "vite build",
+    "lint": "eslint . --report-unused-disable-directives --max-warnings 0",
+    "test": "node --experimental-vm-modules node_modules/.bin/jest"
+  },
+  "devDependencies": {
+    "@eslint/js": "^9.39.2",
+    "@types/jest": "^30.0.0",
+    "@typescript-eslint/eslint-plugin": "^8.54.0",
+    "@typescript-eslint/parser": "^8.54.0",
+    "eslint": "^9.39.2",
+    "globals": "^17.2.0",
+    "jest": "^30.2.0",
+    "ts-jest": "^29.4.6",
+    "ts-node": "^10.9.2",
+    "typescript": "^5.9.3",
+    "vite": "^7.3.1"
+  }
+}